1. Field of the Invention
The present invention relates to new and useful phosphoramidites which are intermediates for polynucleotide synthesis, as well as the improved process for production of oligonucleotides from which polynucleotides are prepared.
2. Description of the Prior Art
Numerous attempts have been made to develop a successful methodology for synthesizing sequence defined oligonucleotides. However, the stepwise synthesis of polynucleotides, and specifically oligonucleotides still remains a difficult and time consuming task, often with low yields. One prior art technique has included the use of organic polymers as supports during polynucleotide synthesis. Classically the major problems with polymer supported synthesis strategies has been inherent in the nature of the polymer support. Various prior art polymers used in such synthesis have proven inadequate for reasons such as: (1) slow diffusion rates of activated nucleotides into the support; (2) excessive swelling of various macroporous, sorption of reagent onto the polymer. See for example, V. Amarnath and A. D. Broom, Chemical Reviews 77, 183-217 (1977).
Modified inorganic polymers are known in the prior art, primarily for use as absorption materials, for example, in liquid chromatography. The attachment of nucleosidephosphates to silica gel using a trityl linking group is described in the prior art (H. Koster, Tetrahedron Letters, 1527-1530, 1972) but the method is apparently applicable only to pyrimidine nucleosides. The cleavage of the nucleoside from the silica support can only be accomplished with acid to which the purine nucleosides are sensitive.
The production of phosphotriester derivatives of oligothymidylates is described in literature (R. L. Letsinger and W. B. Lunsford, Journal of the American Chemical Society, 98:12, 3655-3661) by reaction of a phosphorodichloridite with a 5'-O blocked thymidine and subsequent reaction of the product with a 3'-O blocked thymidine followed by oxidation of the resulting phosphite to a phosphate and removal of blocking groups to obtain the phosphotriesters; using this procedure, the tetramer and pentamer products, dTpTpTpT and dTpTpTpTpT in which T is thymidine were prepared. Unfortunately, the process requires separation and purification of products at each stage to ensure proper sequencing of the added nucleosides Separation techniques including precipitation and washing of precipitates are necessary to implement each successive stage reaction.
In the aforementioned commonly assigned patent application are described methods for forming internucleotide bonds, i.e. bonds linking nucleosides in an oligonucleotide or polynucleotide, by reaction of halophosphoridites with suitably blocked nucleoside or oligonucleotide molecules.
The deoxynucleoside-modified silica gel is condensed with a selected nucleotide through formation of a triester phosphite linkage between the 5' -OH of the deoxynucleoside. The phosphite linkage can be produced by first incorporating the phosphite group onto the 5' -OH of the nucleoside on the silica gel followed by condensation with the added nucleoside through the 3' -OH. Alternatively, and preferably, the phosphite group is incorporated into the added nucleoside at the ' -OH (the 5' -OH being blocked as by tritylating) and the resulting nucleoside phosphite then reacted with the 5' -OH of the nucleoside of the silica gel.
The deoxynucleoside-modified silica gel can also be condensed with a selected nucleoside through formation of a triester phosphite linkage between the 3' -OH of the deoxynucleoside of the silica gel and the 5' -OH of the selected deoxynucleoside. The phosphite linkage can be produced by first incorporating the phosphite group onto the 3' -OH of the nucleoside on the silica gel followed by condensation with the added nucleoside through the 5' -OH. Alternatively and preferably by this approach, the phosp.hite group is incorporated into the added nucleoside at the 5' -OH (3' -OH being blocked as by tritylating using art form procedures) and the resulting nucleoside phosphite then reacted with the 3' -OH of the nucleoside on the silica gel.
The general reaction can be represented by the following: ##STR1##
The preferred reaction is represented as follows: ##STR2## wherein .circle.P is an inorganic polymer linked to the 3' or 5' -O- of the nucleoside through a base hydrolyzable covalent bond; R is H or a blocking group; R.sub.1 ' is a hydrocarbyl radical containing up to 10 carbons; each B is a nucleoside or deoxy-nucleoside base; and each A is H, OH or OR.sub.4 in which R.sub.4 is a blocking group; and X is halogen, preferably Cl or Br or a secondary amino group.
The compounds of structure II and IIa wherein X is a 2.degree. amino group include those in which the amino group is an unsaturated nitrogen heterocycle such as tetrazole, indole, imidazole, benzimidazole and similar nitrogen heterocycles characterized by at least two ethylenic double bonds, normally conjugated, and which may also include other heteroatoms such as N, S or O. These compounds of structure II and IIa wherein X is such a heterocyclic amine, i.e., one in which the amino nitrogen is a ring heteroatom, are characterized by an extremely high reactivity, and consequently relatively low stability, particularly in the indicated preparation of compounds of structure III and IIIa. These phosphoramidites and the corresponding chloridites from which they are prepared are unstable to water (hydrolysis) and air (oxidation). As a consequence, such compounds can only be maintained under inert atmosphefe, usually in sealed containers, at extremely low temperatures generally well below 0.degree. C. Thus, the use of these compounds in the preparation of compounds of structure III and IIIa requires extreme precautions and careful handling due to the aforesaid high reactivity and low stability.
The present new compounds are of structure II and IIa wherein X is a certain type of secondary amino group. Specifically, the present new compounds are those in which X is a saturated secondary amino group, i.e. one in which no double bond is present in the secondary amino radical. More particularly, X is NR.sub.2 'R.sub.3 ', wherein R.sub.2 ' and R.sub.3 ' taken separately each represents alkyl, aralkyl, cycloalkyl and cycloalkylalkyl containing up to 10 carbon atoms, R.sub.2 ' and R.sub.3 ' when taken together form an alkylene chain containing up to 5 carbon atoms in the principal chain and a total of up to 10 carbon atoms with both terminal valence bonds of said chain being attached to the nitrogen atom to which R.sub.2 ' and R.sub.3 ' are attached; and R.sub.2 ' and R.sub.3 ' when taken together with the nitrogen atom to which they are attached form a saturated nitrogen heterocycle including at least one additional heteroatom from the group consisting of nitrogen, oxygen and sulfur.
The present new compounds are not as reactive as those of the aforesaid copending application and not as unstable. However, the present new compounds do react readily with unblocked 3'-OH or 5'-OH of nucleosides under normal conditions. The present new phosphoramidites are stable under normal laboratory conditions to hydrolysis and air oxidation, and are stored as dry, stable powders. Therefore, the present new phosphoramidites are more efficiently employed in the process of forming internucleotide bonds, particularly in automated processing for formation of oligonucleotides and polynucleotides as described in the aforesaid copending application.
Amines from which the group NR.sub.2 R.sub.3 can be derived include a wide variety of saturated secondary amines such as dimethylamine, diethylamine, diisopropylamine, dibutylamine, methylpropylamine, methylhexylamine, methylcyclopropylamine, ethylcyclohexylamine, methylbenzylamine, methycyclohexylmethylamine, butylcyclohexylamine, morpholine, thiomorpholine, pyrrolidine, piperidine, 2,6-dimethylpiperidine, piperazine and similar saturated monocyclic nitrogen heterocycles.
The nucleoside and deoxynucleoside bases represented by B in the above formulae are well-known and include purine derivatives, e.g. adenine, hypoxanthine and guanine, and pyrimidine derivatives, e.g. cytosine, uracil and thymine.
The blocking groups represented by R.sub.4 in the above formulae include trityl, methoxytrityl, dimethoxytrityl, dialkylphosphite, pivalyl, isobutyloxycarbonyl, t-butyl dimethylsilyl, acetyl and similar such blocking groups.
The hydrocarbyl radicals represented by R.sub.1 include a wide variety including alkyl, alkenyl, aryl, aralkyl and cycloalkyl containing up to about 10 carbon atoms. Representative radicals are methyl, butyl, hexyl, phenethyl, benzyl, cyclohexyl phenyl, naphthyl, allyl and cyclobutyl. Of these the preferred are lower alkyl, especially methyl and ethyl.